Hi, new user here. I want to use a custom database (which looks at the ITS region) instead of the standard Silva database, is this possible in Mothur and if so how?
many thanks
Wedwards
update, I have gotten to the align.seqs step of the mothur pipeline. The database file (AF_LSU_v1 Databases – Anaerobic Fungi Network ) I would like to use was a .fna, which i converted to a .fasta using any2fasta. However, when used in the align.seqs step, i still get the error “template is not aligned, aborting”.
I would really like to use mothur for my analysis and i have been told users of the same database (the anaerobic fungi network (AFN)) have had success with mothur, so if anyone knows how i should format the AFN database to work it would be hugely appreciated 
many thanks again
Wedwards
To use the file with align.seqs as a reference, it needs to be aligned first. I really know nothing about ITS sequences which is part of the reason we’ve never posted anything. One alternative would be to use pairwise.align instead which does not require your input sequences to be aligned first.
Pat
Hi Pat
thanks for the response! The database is actually LSU rather than ITS even though its for fungi (odd i know). I will try what you’ve suggested!